/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
catch (Exception ex)\r
{\r
System.out.println(line);\r
- ex.printStackTrace();\r
System.out.println("Error parsing feature file: " + ex +"\n"+line);\r
return false;\r
}\r
return true;\r
}\r
\r
- void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
{\r
+ if(removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>")==-1)\r
+ removeHTML = false;\r
+\r
StringBuffer sb = new StringBuffer();\r
StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
String token, link;\r
+ int startTag;\r
+ String tag=null;\r
while(st.hasMoreElements())\r
{\r
- token = st.nextToken("<>");\r
+ token = st.nextToken("&>");\r
if(token.equalsIgnoreCase("html") || token.startsWith("/"))\r
+ {\r
continue;\r
+ }\r
+\r
+ tag = null;\r
+ startTag = token.indexOf("<");\r
+\r
+ if (startTag > -1)\r
+ {\r
+ tag = token.substring(startTag+1);\r
+ token = token.substring(0, startTag);\r
+ }\r
\r
- if(token.startsWith("a href="))\r
+ if (tag != null && tag.toUpperCase().startsWith("A HREF="))\r
{\r
- link = token.substring(token.indexOf("\"")+1, token.length()-1);\r
+ if(token.length()>0)\r
+ sb.append(token);\r
+ link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);\r
String label = st.nextToken("<>");\r
- sf.addLink(label+"|"+link);\r
- sb.append(label+"%LINK%");\r
+ sf.addLink(label + "|" + link);\r
+ sb.append(label + "%LINK%");\r
}\r
- else if(token.equalsIgnoreCase("br"))\r
+ else if (tag != null && tag.equalsIgnoreCase("br"))\r
sb.append("\n");\r
+ else if (token.startsWith("lt;"))\r
+ sb.append("<" + token.substring(3));\r
+ else if (token.startsWith("gt;"))\r
+ sb.append(">" + token.substring(3));\r
+ else if (token.startsWith("amp;"))\r
+ sb.append("&" + token.substring(4));\r
else\r
+ {\r
sb.append(token);\r
+ }\r
}\r
\r
if(removeHTML)\r
sf.description = sb.toString();\r
+\r
}\r
\r
/**\r
out.append(next[j].type+"\t");\r
else\r
{\r
+ if(next[j].links!=null\r
+ && next[j].getDescription().indexOf("<html>")==-1)\r
+ out.append("<html>");\r
+\r
out.append(next[j].description+" ");\r
if(next[j].links!=null)\r
{\r
+ "</a>");\r
}\r
}\r
+\r
+ if (next[j].getDescription().indexOf("</html>") == -1)\r
+ out.append("</html>");\r
}\r
+\r
+\r
out.append("\t");\r
}\r
\r